Index
NAME
InSilicoSpectro::Utils::io
DESCRIPTION
Miscelaneous I/O utilities.
FUNCTIONS
getFD()
The getFD function takes either a file string, a piped command or a file description as argument and returns a file descriptor. In case of error while opening, it returns undef.
uncompressFile($fname, [\%args])
Uncompresses a gziped file. Returns the new uncompressed file name; Erase the original; %args can overwrite default values
- remove => [1];
- dest => filename [undef];
-
If defined, the uncompressed file is not the original one =~s/\.gz$//i, but it has this file name.
headGz($fname, [$nblines], [$re])
Uncompresses file $fname and takes the $nblines first lines (default 10) satisfying regular expression $re (if defined).
Returns either an array or lines concatenated with \n characters, depending on the context.
compressFile($fname, [\%args])
Compresses to a gziped file. Returns the new compressed file name; Erases the original by default; %args can overwrite default values.
- remove => [1];
zipFiles($dest, \@files, [$baseNameOnly])
Opens a zip archive $dest and puts all the files contained in @files into it. $dest can be either undef (means STDOUT), or a filehandle, or a file name. If($baseNameOnly) [default undef], stores the file under its basename (removes directory name).
getMD5($file)
Returns a MD5 checksum of $file.
croakIt($msg)
Croaks with the given message, but appends a stack trace if $InSilicoSpectro::Utils::io::VERBOSE is true.
COPYRIGHT
Copyright (C) 2004-2005 Geneva Bioinformatics www.genebio.com
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
AUTHORS
Alexandre Masselot, www.genebio.com